Different medical treatment choices may affect the health of patients with chronic diseases. This study aims to assess the relationship between treatment choices, including the use of traditional Chinese medicine (TCM), and the health levels of middle-aged and elderly patients with six chronic diseases. The sample data comes from China Health and Retirement Longitudinal Study (CHARLS 2018). Basic conditions, medical choices and health status of patients are incorporated. The ordered Logit and Logit regression models are used to analyze and compare the effects of six chronic disease patients’ medical options on their self-rated health (SRH) and depression. The overall average score of SRH is the highest in patients with heart disease (the worst in SRH), which is 3.433. Arthritis patients have the highest overall depression average score (depression) at 0.444. Under the premise of controlling a variety of socio-demographic factors, compared with the non-treatment group, taking TCM has a significant positive effect on SRH of patients with five diseases except hypertension. Both taking western medicine (WM) and taking integrated Chinese and Western medicine (IM) have a significant positive effect on SRH scores of patients with six chronic diseases in middle and old age. Taking TCM has effect on depression of patients with heart or stomach diseases, and taking WM and IM affects depression of middle-aged and elderly chronic patients except diabetes. Taking IM has a greater effect on SRH and depression of chronically ill patients, followed by taking WM, and the effect of taking TCM is relatively small, which is related to the development stage of the disease. Therefore, in the future, the control and treatment of chronic diseases in the middle and late stages can be discussed from the perspective of integrated traditional Chinese and western medicine, but attention should be paid to drug interactions. In order to improve the treatment rate and health level of patients with chronic diseases, their economic burden should be reduced, and they should be guided to choose more reasonable treatment methods.